Ian Blavins wrote:
. . .
When I reach a recognisable state I copy the (Netbeans) development folder into my Product Versions folder, rename the copy with the next version number, and ask time machine to do a backup.
. . .
Recently I have noticed that the Product Versions folder in TM does not contain all the version folders that are on the internal disk. I have asked TM to make a new backup a couple of times and it continues to ignore the version folders it doesn't have.
I'm not familiar with Netbeans. It's possible that (like Apple's Xcode) it puts an extended attribute on some such items to exclude them from backups. See the yellow box in Time Machine - Frequently Asked Question #11 for a way to tell if that's the situation.
One thing that may be confusing TM is that the copies of the development folder in the product versions folders all have the same last-modified date. Presumably this is because during software development I am changing the contents of files and folders in the development folder, but not the structure of the folder itself, so its last-modified date isn't being changed.
That shouldn't matter. Ordinarily, Time Machine uses the File System Event Store, a log of changes to the file system, to determine which folders have been changed and have contents that need to be backed-up.
I have done what was done above - create a text file, put it in a new folder, and copy the folder into the version folders that are not being backed up.
Did you make the files with a standard app (that won't be marking things to be excluded)?
Just to add some spice to this, I run a two TM disk backup scheme. I use one TM disk for about a day and then swap it out for the othe disk. I do this about dinner time since the first backup to the newly swapped in drive is likely to be a large one. I just did a swap. Not only did the some of the product version folders not get copied, there were more that weren't copied than with the other disk.
Each set of backups should be independent; when a backup is run, Time Machine should back up the changes since the previous backup to that particular volume.
I'm not sure about your folder structure or what is, and is not, getting backed-up: is it possible that no changes to particular folders have been backed-up recently, or are some backed-up and others missed?
If no changes to a particular folder are getting backed-up, and you don't find the extended attributes above, that folder may be damaged. That's rare, and we don't know what the actual damage is, but it does happen. If so, the only known fix is to create a new folder, copy the contents of the damaged one into it, then delete the damaged one.
Another thing you might try is starting from your Snow Leopard Install disc and repairing your internal HD. Whether it needs it or not, that will usually trigger a "deep traversal" on the next backup, where Time Machine doesn't use the File System Event Store, but compares everything on your system to the most recent completed backup. (You'll see "scanning nnnn items" messages on the Time Machine Preferences window.)
Unless the extended attribute is set to ignore the folder, that should "catch up" with all the changes.